Once the Fred/Roscoe/Sofia/Sorrel
combination formed, positive feedback would have ensured that more
of each were created, and puddle evolution would have gradually
improved the effectiveness of the Fred and Sofia enzymes.
As the tides rolled and the waves splashed,
Freds, Roscoes, Sofias and Sorrels would have gradually spread into
neighboring puddles and pools. Some would have splashed into the
open ocean and drifted on currents to new locations many kilometers
from their origins.
We can consider this to be the first explosion-- a
dispersal event that invades a larger geographical area with a new
and improved form of life (or in this case, preliminary partial maybe
sort-of almost life forms).
Let's take a closer look at what would have happened to our
first self-replicating chemicals, as they diffused into new regions,
far from their home.
First of all, Fred and Roscoe would have
been completely useless in the open ocean, or in any large body of
water. The problem is that they were still only capable of choosing
between two different types of molecules. That was good enough in
the home puddle, with its high concentration of just two specific
amino acids and two chain molecules. However, in the open ocean,
there would have been many different types of molecules that were
similar to the components of Fred, Roscoe, Sofia and Sorrel. The
result is that Fred and Roscoe would have merely produced chains
with a completely random sequence of many molecules, making them
At this stage of chemical evolution, pretty
much anything would act as a 'poison' to our primitive
Not only that, but the Fred/Roscoe/Sofia/Sorrel
combination had a very basic problem, when it came to surviving far
from the home puddle. Because they were four separate molecules,
that had to all get to the same place at the same time in order to
work . It's plausible to imagine a single Fred or Sofia drifting
and diffusing into a hospitable place far from home, but much less
likely for all the necessary molecules to get there.
Even worse, they were just small raw molecules,
all alone in a hostile sea that was full
of all sorts of hazards. There would have been volcanic hot spots,
and enzymatic blobs, metal
ions, ultraviolet radiation, gamma rays and
radioactive decay particles-- all
of them poised to decompose a Fred or a Sofia back into its individual
It's probably too much to expect that a complete set of the
Fred/Roscoe/Sofia/Sorrel components would ever drift kilometers from
home, with any chance of success. But closer to home, they probably
would have managed to drift into an occasional new shoreline pool
or puddles, all at the same time.
What happened next would depend on the contents
of the puddle.
Nearly all of the puddles and pools along
the primeval coastlines would have contained a mixture of many different
amino acids and chain molecules, similar to the open ocean. They
would have been entirely poisonous to any Freds or Roscoes that drifted
Likewise, some puddles would have contained
a shortage of amino acids or chain molecules, perhaps because they
were washed clean by rainwater, or had their organic contents removed
by some natural process. Those puddles would have starved any Freds
or Roscoes that happened to arrive there.
Many puddles would also have contained catalysts
or chemical agents that would decompose large chains. Those locations
would merely add Fred or Sofia back to the soup, in the form of single
amino acids or chain molecules.
Finally, an occasional puddle may have contained
high concentrations of just two amino acids and just two chain molecules,
similar to the home puddle. However, in nearly all cases, those molecules
would have been too different from the normal constituents of our
four chains. Fred and Roscoe might still have managed to duplicate
new amino acids and chains in the new puddle. However, the resulting
compounds would be very different from the originals, with very different
chemical properties. Because of that, the children would not be effective
Freds, Roscoes, Sofias or Sorrels, and self-replication would cease.
On the opposite extreme, there may have been
a few rare puddles and pools that contained high concentrations of
the same, original two amino acids and two chain molecules as in
the first Fred puddle. Once a Fred, a Sofia and a Sorrel simultaneously
diffused into such a puddle, they would create another production
center, and start flooding their own neighborhood with Freds, Roscoes,
Sofias and Sorrels.
Of course, the first home puddle was just
a very small puddle on the edge of a huge ocean. It probably wasn't
producing that many Freds, Sofias and Sorrels, and it is unlikely
that they would have simultaneously diffused over a very long distance.
However, it's possible that by some quirk of chemistry, there
were similar puddles relatively close by. Or perhaps a full set of
self-replicating molecules may have been engulfed by a glob of natural
tar or mucus, and then traveled together to a distant heavenly puddle.
It's nice to think of new little colonies of Freds starting
up, even at this early stage of proto-life. But as hopeful as it
may seem, those new colonies would not actually have had much affect
on the pace of evolution. After all, they were merely identical to
the home puddle. All they would have done is increase the global
concentrations of self-replicating compounds, by a little.
Pretty Good Puddles
In between the deadly puddles and the perfect
ones, there may have been a few puddles with intermediate conditions.
For example, a 'pretty good' puddle might contain the
same chain molecules as the original Fred puddle, and one of the
same amino acids-- but have one amino acid component that was
similar to the original, but just a little different.
Roscoe would work fine there, and Fred could
probably replicate new polypeptides there too, though they wouldn't
be effective Freds. However, such a 'pretty good' puddle
would still have been extremely interesting-- since it could
help our 'life-like' chemicals to evolve into new forms.
Let's take a closer look at that now.
New Raw Materials
Let's consider a 'pretty good' puddle with a concentration
of three of the four 'home puddle' molecules, along with
a high concentration of something else.
For example, we built our first Fred example
from leucine and lysine (two modern amino acids), but a Fred, Sofia
and Sorrel may have one day diffused into a nearby puddle that contained
high concentrations of leucine and 5-methyl-lysine instead (almost
the same molecule, but with a side chain containing an extra carbon).
In that new puddle, Fred would still read
Sofia, but it would produce a new amino acid chain built from a slightly
If the new molecule was similar enough to
the old, it might not have much impact on the folding or chemical
action of Fred. Which means that the new proteins transcribed by
Fred in the new environment might work passably well on their own.
Even if the change did have some impact,
it's possible that a mutant form of Sofia would 'undo' the
chemical and structural changes caused by the new molecules, and
create a fully functional Fred using the new components. Since the
chemical change in the raw materials was small, the genetic change
to compensate for it might also be small.
The result would have been a mildly different
version of Fred that we'll call an alt-Fred. This new molecule
would work with the new combination of components, and it would be
created by a chain that we'll call alt-Sofia (with a slightly
different sequence from the original Sofia).
Of course, the same kind of 'chemical drift' could also
occur in the chain molecules used as raw materials by Roscoe. Consider
a puddle the contained the original two amino acids, plus one of
the original chain molecules, and another that was just a wee bit
different from its original.
If the difference wasn't too extreme, Roscoe could probably
still 'read' the difference between the two types of
chain molecules, and still link chain molecules in approximately
the right order at its knee. It probably wouldn't work nearly
as well as with the original molecules, but it might eventually mutate
into an alt-Roscoe (coded by an alt-Sorrel) that would work better.
Since Fred also was affected by changes in
the chain composition, a change of chain molecules would also result
in an alt-Fred (coded by an alt-Sofia) that would be a bit different
at its elbow end.
Almost Perfect Puddles
Of course these gradual changes the chemistry
of Fred and Sofia would have worked best in puddles that contained
three raw materials that were exactly the same as in the 'home
puddle', and a fourth compound that was only a little bit different.
That kind of slightly-different puddle would actually have been much
more common than puddles with exactly the same raw materials as in
the original Fred puddle.
There are four possible raw materials that
could have been different in a 'favorable' puddle, and
perhaps a half-dozen chemical variations in each ingredient that
might have been similar enough so an alt-Fred or alt-Sofia could
have evolved into using them.
That means that there would have been approximately
24 times as many 'almost perfect' puddles as perfect
Once a new alt-Fred and alt-Sofia formed
from a slightly different set of raw materials, they in turn could
have colonized other nearby puddles. Each time a new 'almost
perfect' puddle was colonized, one of the raw materials might
have shifted slightly, creating a new alt-Fred, alt-Roscoe, alt-Sofia
and alt-Sorrel combination that could self-replicate, using slightly
After a sufficient number of evolutionary
jumps like that, there would eventually have
been a new set of alt-Fred, alt-Roscoe,
alt-Sofia and alt-Sorrel molecules
which could self-replicate from amino
acids and chain molecules that
were entirely different from the originals.
Given enough time and enough 'almost perfect' puddles,
new versions of alt-Fred and alt-Sofia could have gradually evolved
into use of extremely different components, one small chemical step
at a time.
The alt-ification of Fred and Roscoe wouldn't have increased
their ability to exist outside of puddles that had the right concentrations
of contents. But it would have allowed them to expand into more just-right
puddles that contained different chemistry.
The evolution of Fred and Roscoe into alt-Freds
and alt-Roscoes may have also been assisted by chemical gradients between two sets of pools. The right gradients might have allowed
Fred or Sofia to start using new raw materials more quickly, by providing
For example, let's look at the formation of Freds in a puddle
complex that contains a gradient in one of the amino acids contained
in Fred. At the north end is a high concentration of glutamate (E,
polar), and at the south end is a high concentration of aspartate
(D, polar). In between are many small puddles and micro-puddles containing
different combinations of the two molecules.
These two molecules have similar chemical
properties, but aspartate is a wee bit bigger, with one extra carbon.
In the north, Fred would read a Sofia and
create more Freds built from leucine and glutamate, just like normal.
In the south, Fred would create mutant proteins
built from leucine and aspartate that would
be so different that they would not function
Somewhere in between, Fred would find itself
in a chemical mix with both glutamate and
asparatate. If it were close to the glutamate
side of the gradient, it might build structures
with just a couple of aspartate substitutions,
This new polypeptide would have a slightly
different shape than the original Fred, but
it's possible that it would still have
some or all of Fred's functionality,
since there was only a difference of a couple
of atoms, and the locations of charged area
was still exactly the same.
Now there would be puddle evolution that
would select for Sofias that created Freds
with a more reliable structure that functioned
well, even with a few random arginines substituted
into the chain. That might mean an adjustment
in the chain sequence. Likewise, puddle evolution
would tend to produce new versions of Sorrel
in the intermediate zone that created effective
Roscoes, even when aspartate substituted
for some of the glutamates.
Some of the new aspartate-tolerant Freds
and Roscoes might then in turn diffuse further
south into a higher-aspartate neighborhood,
and make a further jump into aspartate tolerance.
With enough time and enough small puddles
in the gradient, the end result might be
an alt-Fred and alt-Roscoe that were built
completely from aspartate instead of glutamate
(along with the alt-Sofia and alt-Sorrel
chains that produced them).
In a world of puddles that had different
concentrations of amino acids, there would
have been many gradients like this, and they
would have provided a second way that alt-Freds
and alt-Sofias could have evolved from the
We have talked about Fred and Roscoe using
polar and non-polar (hydrophobic) amino acids
for their action, since proteins typically
use both types of amino acids to build a
chemically effective enzyme .
If an alt-Fred contained different molecules,
but the same arrangement of polar and non-polar
amino acids, it would already have a head
start on the correct structure to work effectively.
There might need to be some small changes
to compensate for the different size of the
new molecules, but that would only require
some small changes in sequence, so it could
act like the original.
You might think of Fred's structure
as a combination of different 'domains',
some of them hydrophobic, some polar, and
some a combination. An alt-Fred simply needed
to fill the same domains with similar structures,
using a different set of molecules.
You might notice that the appearance of alt-Fred
variations would create an additional sort
of genetic selection for our extremely primitive
If an alt-Fred developed that used a pair
of amino acids that gave those alt-proteins
some kind of advantage over other alt-proteins,
then organisms based on that particular set
of proteins would have spread further and
faster than the other Fred variations.
Likewise, if a pair of chain molecules created
genetic chains that were particularly good,
those alt-chains would have become established
at a faster rate than other Sofia progeny.
The selective advantage for the early proteins
and chains might have been ease of synthesis,
or chemical stability, or effective catalysis.
The shifting towards more effective chemistry
for Fred and Sofia could have started during
the first explosion, and it would have increased
during later explosions as more and more
effective organisms developed.
In other words, even if the first Fred was
based on a poor choice of amino acids, it
would have eventually been replaced by a
superior alt-Fred that used more effective
Chicken and Egg
Many past efforts to explain early biogenesis
have relied on one chemical class to provide
two functions in the earliest chemical stage
of evolution. The 'RNA world' hypothesis
puts RNA in both information-carrying and
catalytic roles, and various other theories
have proposed some sort of information-carrying
role for proteins or other substances.
One big advantage of the Fred/Sofia system
that we have discussed so far, is that it's
a lot like life, right from the beginning.
Fred and Sofia still have a long ways to
go before they are completely life-like,
but all of the subsequent evolutionary steps
can proceed with a similar division of labor.
There is no need for an awkward switch from
one chemical system to another.